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- PDB-5cch: Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short ... -

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Basic information

Entry
Database: PDB / ID: 5cch
TitleStructure of the Ca2+-bound synaptotagmin-1 SNARE complex (short unit cell form)
Components
  • (Synaptosomal-associated protein ...) x 2
  • Synaptotagmin-1
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2
KeywordsENDOCYTOSIS / EXOCYTOSIS / synaptic fusion complex / Synaptotagmin1 / neuronal SNARE complex
Function / homology
Function and homology information


exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of vesicle fusion / regulation of delayed rectifier potassium channel activity / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion ...exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of vesicle fusion / regulation of delayed rectifier potassium channel activity / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion / BLOC-1 complex / calcium-dependent activation of synaptic vesicle fusion / Lysosome Vesicle Biogenesis / myosin head/neck binding / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane / zymogen granule membrane / storage vacuole / synaptic vesicle fusion to presynaptic active zone membrane / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / extrinsic component of presynaptic membrane / calcium ion-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / Glutamate Neurotransmitter Release Cycle / calcium ion sensor activity / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / eosinophil degranulation / Golgi Associated Vesicle Biogenesis / regulation of synaptic vesicle priming / regulation of establishment of protein localization / vesicle-mediated transport in synapse / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / exocytic vesicle / positive regulation of intracellular protein transport / positive regulation of calcium ion-dependent exocytosis / vesicle organization / vesicle docking / protein heterooligomerization / ribbon synapse / positive regulation of dendrite extension / regulation of vesicle-mediated transport / Cargo recognition for clathrin-mediated endocytosis / secretion by cell / positive regulation of dopamine secretion / regulation of exocytosis / SNAP receptor activity / chloride channel inhibitor activity / SNARE complex / Clathrin-mediated endocytosis / vesicle fusion / calcium-ion regulated exocytosis / actomyosin / LGI-ADAM interactions / hormone secretion / dense core granule / Golgi to plasma membrane protein transport / positive regulation of hormone secretion / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / ATP-dependent protein binding / neurotransmitter secretion / protein localization to membrane / regulation of synaptic vesicle recycling / syntaxin binding / clathrin-coated vesicle / presynaptic active zone / syntaxin-1 binding / insulin secretion / endosomal transport / Neutrophil degranulation / SNARE complex assembly / low-density lipoprotein particle receptor binding / positive regulation of neurotransmitter secretion / clathrin binding / neurotransmitter transport / phosphatidylserine binding / synaptic vesicle priming / regulation of synapse assembly / response to gravity / myosin binding / regulation of neuron projection development / regulation of dopamine secretion / regulation of synaptic vesicle exocytosis / exocytosis / modulation of excitatory postsynaptic potential / positive regulation of exocytosis / synaptic vesicle exocytosis
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Synaptotagmin / Synaptosomal-associated protein 25 / SNAP-25 domain ...Synaptobrevin/Vesicle-associated membrane protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Synaptotagmin / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Synaptotagmin-1 / Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsZhou, Q. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Weis, W.I. / Brunger, A.T.
CitationJournal: Nature / Year: 2015
Title: Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis.
Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. ...Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. / Lemke, H.T. / Pfuetzner, R.A. / Choi, U.B. / Weis, W.I. / Diao, J. / Sudhof, T.C. / Brunger, A.T.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Derived calculations
Revision 1.3Sep 16, 2015Group: Database references
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Synaptotagmin-1
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,34513
Polymers96,0656
Non-polymers2817
Water00
1
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Synaptotagmin-1
F: Synaptotagmin-1
hetero molecules

F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,75318
Polymers128,3127
Non-polymers44111
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)69.073, 171.626, 146.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN E
211CHAIN F
DetailsAuthors state that the biological assembly includes Chain A, B, C, D, Chain E 273-421, Chain F 273-421, Chain F 141-265 from symmetric neighbor.

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Components

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Protein , 3 types, 4 molecules ABEF

#1: Protein Vesicle-associated membrane protein 2 / VAMP-2 / Synaptobrevin-2


Mass: 7231.061 Da / Num. of mol.: 1 / Fragment: UNP residues 28-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vamp2, Syb2 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63045
#2: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 7837.957 Da / Num. of mol.: 1 / Fragment: UNP residues 191-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32851
#5: Protein Synaptotagmin-1 / Synaptotagmin I / SytI / p65


Mass: 32247.197 Da / Num. of mol.: 2 / Fragment: UNP residues 141-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21707

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Synaptosomal-associated protein ... , 2 types, 2 molecules CD

#3: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 9030.114 Da / Num. of mol.: 1 / Fragment: UNP residues 7-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60881
#4: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 7471.368 Da / Num. of mol.: 1 / Fragment: UNP residues 141-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snap25, Snap / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60881

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Non-polymers , 1 types, 7 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.56 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 20922 / % possible obs: 99.7 % / Redundancy: 14.5 % / Biso Wilson estimate: 133.06 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Rrim(I) all: 0.105 / Χ2: 0.584 / Net I/av σ(I): 24.6 / Net I/σ(I): 4 / Num. measured all: 302949
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.7312.40.74120170.8950.2520.9480.43798.7
3.73-3.8813.30.66520780.9460.1810.690.45299.8
3.88-4.0513.80.43820550.9750.1180.4540.473100
4.05-4.2714.30.28120610.9880.0750.2910.52599.9
4.27-4.5415.70.19120590.9950.0490.1980.56799.9
4.54-4.8915.60.14720820.9970.0380.1520.616100
4.89-5.3814.80.12220980.9980.0320.1260.643100
5.38-6.1515.60.12820930.9970.0330.1320.59999.4
6.15-7.7515.20.08121410.9990.0210.0840.662100
7.75-5014.10.04822380.9980.0130.050.79499.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N7S,3F04,1UOW

1n7s

3f04

1uow


Resolution: 3.6→48.29 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.289 1085 5.2 %
Rwork0.249 --
obs0.251 20850 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 157.7 Å2
Refinement stepCycle: LAST / Resolution: 3.6→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6321 0 7 0 6328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046609
X-RAY DIFFRACTIONf_angle_d0.8628902
X-RAY DIFFRACTIONf_dihedral_angle_d11.2272512
X-RAY DIFFRACTIONf_chiral_restr0.04993
X-RAY DIFFRACTIONf_plane_restr0.0041158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11E2390X-RAY DIFFRACTIONPOSITIONAL
12F2390X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5988-3.76260.43171390.4082360X-RAY DIFFRACTION98
3.7626-3.96090.37861240.3242445X-RAY DIFFRACTION100
3.9609-4.20890.32081360.27692447X-RAY DIFFRACTION100
4.2089-4.53360.28661250.25412463X-RAY DIFFRACTION100
4.5336-4.98940.24081310.232466X-RAY DIFFRACTION100
4.9894-5.71040.26761450.24012453X-RAY DIFFRACTION99
5.7104-7.19070.33171430.2772506X-RAY DIFFRACTION100
7.1907-48.2960.25421420.21082625X-RAY DIFFRACTION99

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